musica 0.12.0__cp39-cp39-macosx_11_0_arm64.whl → 0.12.1__cp39-cp39-macosx_11_0_arm64.whl

musica/mechanism_configuration/condensed_phase_arrhenius.py

@@ -1,13 +1,17 @@
-from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _CondensedPhaseArrhenius, _ReactionComponent
-from .phase import Phase
-from .species import Species
+from ..constants import BOLTZMANN
+from .utils import _add_other_properties
 from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties, _remove_empty_keys
-from musica.constants import BOLTZMANN
+from .species import Species
+from .phase import Phase
+from typing import Optional, Any, Dict, List, Union, Tuple
+from .. import backend
 
+_backend = backend.get_backend()
+_CondensedPhaseArrhenius = _backend._mechanism_configuration._CondensedPhaseArrhenius
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
 
-class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
+
+class CondensedPhaseArrhenius:
     """
     A class representing a condensed phase Arrhenius rate constant.
 
@@ -21,8 +25,7 @@ class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
         E (float): Pressure scaling term [Pa-1].
         reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
         products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_water (Species): The water species in the aerosol phase.
+        condensed_phase (Phase): The condensed phase in which the reaction occurs.
         other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase Arrhenius rate constant.
     """
 
@@ -35,10 +38,10 @@ class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
         Ea: Optional[float] = None,
         D: Optional[float] = None,
         E: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        reactants: Optional[List[Union[Species,
+                                       Tuple[float, Species]]]] = None,
         products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_water: Optional[Species] = None,
+        condensed_phase: Optional[Phase] = None,
         other_properties: Optional[Dict[str, Any]] = None,
     ):
         """
@@ -54,21 +57,39 @@ class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
             E (float): Pressure scaling term [Pa-1].
             reactants (List[Union[Species, Tuple[float, Species]]]]: A list of reactants involved in the reaction.
             products (List[Union[Species, Tuple[float, Species]]]]: A list of products formed in the reaction.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_water (Species): The water species in the aerosol phase.
+            condensed_phase (Phase): The condensed phase in which the reaction occurs.
             other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase Arrhenius rate constant.
         """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.A = A if A is not None else self.A
-        self.B = B if B is not None else self.B
+        # Create the internal C++ instance
+        self._instance = _CondensedPhaseArrhenius()
+
+        # Store Python objects for reactants, products, phases
+        self._reactants = reactants if reactants is not None else []
+        self._products = products if products is not None else []
+        self._condensed_phase = condensed_phase
+        self._other_properties = other_properties if other_properties is not None else {}
+
+        # Set basic properties on the C++ instance
+        if name is not None:
+            self._instance.name = name
+        if A is not None:
+            self._instance.A = A
+        if B is not None:
+            self._instance.B = B
         if C is not None and Ea is not None:
             raise ValueError("Cannot specify both C and Ea.")
-        self.C = -Ea / BOLTZMANN if Ea is not None else C if C is not None else self.C
-        self.D = D if D is not None else self.D
-        self.E = E if E is not None else self.E
-        self.reactants = (
-            [
+        if Ea is not None:
+            self._instance.C = -Ea / BOLTZMANN
+        elif C is not None:
+            self._instance.C = C
+        if D is not None:
+            self._instance.D = D
+        if E is not None:
+            self._instance.E = E
+
+        # Set reactants on the C++ instance
+        if reactants is not None:
+            self._instance.reactants = [
                 (
                     _ReactionComponent(r.name)
                     if isinstance(r, Species)
@@ -76,11 +97,10 @@ class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
                 )
                 for r in reactants
             ]
-            if reactants is not None
-            else self.reactants
-        )
-        self.products = (
-            [
+
+        # Set products on the C++ instance
+        if products is not None:
+            self._instance.products = [
                 (
                     _ReactionComponent(p.name)
                     if isinstance(p, Species)
@@ -88,29 +108,202 @@ class CondensedPhaseArrhenius(_CondensedPhaseArrhenius):
                 )
                 for p in products
             ]
-            if products is not None
-            else self.products
-        )
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_water = (
-            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
-        )
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
 
-    @staticmethod
-    def serialize(instance) -> Dict:
+        # Set phase information on the C++ instance
+        if condensed_phase is not None:
+            self._instance.condensed_phase = condensed_phase.name
+        if other_properties is not None:
+            self._instance.other_properties = other_properties
+
+    def __getattr__(self, name):
+        """Delegate unknown attribute access to the internal instance."""
+        return getattr(self._instance, name)
+
+    @property
+    def type(self):
+        """The reaction type."""
+        return self._instance.type
+
+    @property
+    def name(self) -> str:
+        """The name of the condensed phase Arrhenius rate constant."""
+        return self._instance.name
+
+    @name.setter
+    def name(self, value: str):
+        self._instance.name = value
+
+    @property
+    def A(self) -> float:
+        """Pre-exponential factor [(mol m-3)^(n-1)s-1]."""
+        return self._instance.A
+
+    @A.setter
+    def A(self, value: float):
+        self._instance.A = value
+
+    @property
+    def B(self) -> float:
+        """Temperature exponent [unitless]."""
+        return self._instance.B
+
+    @B.setter
+    def B(self, value: float):
+        self._instance.B = value
+
+    @property
+    def C(self) -> float:
+        """Exponential term [K-1]."""
+        return self._instance.C
+
+    @C.setter
+    def C(self, value: float):
+        self._instance.C = value
+
+    @property
+    def D(self) -> float:
+        """Reference Temperature [K]."""
+        return self._instance.D
+
+    @D.setter
+    def D(self, value: float):
+        self._instance.D = value
+
+    @property
+    def E(self) -> float:
+        """Pressure scaling term [Pa-1]."""
+        return self._instance.E
+
+    @E.setter
+    def E(self, value: float):
+        self._instance.E = value
+
+    @property
+    def reactants(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """A list of reactants involved in the reaction."""
+        return self._reactants
+
+    @reactants.setter
+    def reactants(self, value: List[Union[Species, Tuple[float, Species]]]):
+        self._reactants = value
+        # Update the C++ instance
+        self._instance.reactants = [
+            (
+                _ReactionComponent(r.name)
+                if isinstance(r, Species)
+                else _ReactionComponent(r[1].name, r[0])
+            )
+            for r in value
+        ]
+
+    @property
+    def products(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """A list of products formed in the reaction."""
+        return self._products
+
+    @products.setter
+    def products(self, value: List[Union[Species, Tuple[float, Species]]]):
+        self._products = value
+        # Update the C++ instance
+        self._instance.products = [
+            (
+                _ReactionComponent(p.name)
+                if isinstance(p, Species)
+                else _ReactionComponent(p[1].name, p[0])
+            )
+            for p in value
+        ]
+
+    @property
+    def condensed_phase(self) -> Phase:
+        """The condensed phase in which the reaction occurs."""
+        return self._condensed_phase
+
+    @condensed_phase.setter
+    def condensed_phase(self, value: Phase):
+        self._condensed_phase = value
+        # Update the C++ instance
+        self._instance.condensed_phase = value.name if value is not None else ""
+
+    @property
+    def other_properties(self) -> Dict[str, Any]:
+        """A dictionary of other properties of the condensed phase Arrhenius rate constant."""
+        return self._other_properties
+
+    @other_properties.setter
+    def other_properties(self, value: Dict[str, Any]):
+        self._other_properties = value
+        # Update the C++ instance
+        self._instance.other_properties = value
+
+    def serialize(self) -> Dict:
+        """
+        Serialize the CondensedPhaseArrhenius instance to a dictionary.
+
+        Returns:
+            Dict: A dictionary representation of the condensed phase Arrhenius rate constant.
+        """
+        # Convert Python reactants/products to serializable format
+        def serialize_python_components(components):
+            result = []
+            for component in components:
+                if isinstance(component, Species):
+                    result.append(component.name)
+                elif isinstance(component, tuple) and len(component) == 2:
+                    # Handle (coefficient, Species) tuples
+                    coefficient, species = component
+                    result.append({
+                        "species name": species.name,
+                        "coefficient": coefficient
+                    })
+                else:
+                    # Fallback: treat as Species
+                    result.append(component.name if hasattr(component, 'name') else str(component))
+            return result
+
         serialize_dict = {
             "type": "CONDENSED_PHASE_ARRHENIUS",
-            "name": instance.name,
-            "A": instance.A,
-            "B": instance.B,
-            "C": instance.C,
-            "D": instance.D,
-            "E": instance.E,
-            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
-            "products":  ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
-            "aerosol phase": instance.aerosol_phase,
-            "aerosol-phase water": instance.aerosol_phase_water,
+            "name": self.name,
+            "A": self.A,
+            "B": self.B,
+            "C": self.C,
+            "D": self.D,
+            "E": self.E,
+            "reactants": serialize_python_components(self._reactants),
+            "products": serialize_python_components(self._products),
+            "condensed phase": self._condensed_phase.name if self._condensed_phase is not None else "",
         }
-        _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        _add_other_properties(serialize_dict, self._other_properties)
+        return serialize_dict
+
+    @staticmethod
+    def serialize_static(instance) -> Dict:
+        """
+        Static serialize method for backward compatibility.
+
+        Args:
+            instance: The CondensedPhaseArrhenius instance to serialize (can be Python wrapper or C++ type).
+
+        Returns:
+            Dict: A dictionary representation of the condensed phase Arrhenius rate constant.
+        """
+        # Check if it's the new composition-based Python wrapper
+        if hasattr(instance, '_instance'):
+            # New Python wrapper - use instance method
+            return instance.serialize()
+        else:
+            # Old C++ wrapper type - use direct attribute access
+            serialize_dict = {
+                "type": "CONDENSED_PHASE_ARRHENIUS",
+                "name": instance.name,
+                "A": instance.A,
+                "B": instance.B,
+                "C": instance.C,
+                "D": instance.D,
+                "E": instance.E,
+                "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
+                "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
+                "condensed phase": instance.condensed_phase,
+            }
+            _add_other_properties(serialize_dict, instance.other_properties)
+            return serialize_dict

musica/mechanism_configuration/condensed_phase_photolysis.py

@@ -1,10 +1,13 @@
-from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _CondensedPhasePhotolysis, _ReactionComponent
-from .phase import Phase
-from .species import Species
+from .utils import _add_other_properties
 from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties, _remove_empty_keys
+from .species import Species
+from .phase import Phase
+from typing import Optional, Any, Dict, List, Union, Tuple
+from .. import backend
 
+_backend = backend.get_backend()
+_CondensedPhasePhotolysis = _backend._mechanism_configuration._CondensedPhasePhotolysis
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
 
 
 class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
@@ -16,8 +19,7 @@ class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
         scaling_factor (float): The scaling factor for the photolysis rate constant.
         reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
         products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
-        aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-        aerosol_phase_water (float): The water species in the aerosol phase [unitless].
+        condensed_phase (Phase): The condensed phase in which the reaction occurs.
         other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase photolysis reaction rate constant.
     """
 
@@ -25,10 +27,10 @@ class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
         self,
         name: Optional[str] = None,
         scaling_factor: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        reactants: Optional[List[Union[Species,
+                                       Tuple[float, Species]]]] = None,
         products: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
-        aerosol_phase: Optional[Phase] = None,
-        aerosol_phase_water: Optional[Species] = None,
+        condensed_phase: Optional[Phase] = None,
         other_properties: Optional[Dict[str, Any]] = None,
     ):
         """
@@ -39,8 +41,7 @@ class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
             scaling_factor (float): The scaling factor for the photolysis rate constant.
             reactants (List[Union[Species, Tuple[float, Species]]]): A list of reactants involved in the reaction.
             products (List[Union[Species, Tuple[float, Species]]]): A list of products formed in the reaction.
-            aerosol_phase (Phase): The aerosol phase in which the reaction occurs.
-            aerosol_phase_water (Species): The water species in the aerosol phase [unitless].
+            condensed_phase (Phase): The condensed phase in which the reaction occurs.
             other_properties (Dict[str, Any]): A dictionary of other properties of the condensed phase photolysis reaction rate constant.
         """
         super().__init__()
@@ -70,10 +71,7 @@ class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
             if products is not None
             else self.products
         )
-        self.aerosol_phase = aerosol_phase.name if aerosol_phase is not None else self.aerosol_phase
-        self.aerosol_phase_water = (
-            aerosol_phase_water.name if aerosol_phase_water is not None else self.aerosol_phase_water
-        )
+        self.condensed_phase = condensed_phase.name if condensed_phase is not None else self.condensed_phase
         self.other_properties = other_properties if other_properties is not None else self.other_properties
 
     @staticmethod
@@ -84,8 +82,7 @@ class CondensedPhasePhotolysis(_CondensedPhasePhotolysis):
             "scaling factor": instance.scaling_factor,
             "reactants": ReactionComponentSerializer.serialize_list_reaction_components(instance.reactants),
             "products": ReactionComponentSerializer.serialize_list_reaction_components(instance.products),
-            "aerosol phase": instance.aerosol_phase,
-            "aerosol-phase water": instance.aerosol_phase_water,
+            "condensed phase": instance.condensed_phase,
         }
         _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        return serialize_dict

musica/mechanism_configuration/emission.py

@@ -1,9 +1,13 @@
-from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _Emission, _ReactionComponent
-from .phase import Phase
-from .species import Species
+from .utils import _add_other_properties
 from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties, _remove_empty_keys
+from .species import Species
+from .phase import Phase
+from typing import Optional, Any, Dict, List, Union, Tuple
+from .. import backend
+
+_backend = backend.get_backend()
+_Emission = _backend._mechanism_configuration._Emission
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
 
 
 class Emission(_Emission):
@@ -64,4 +68,4 @@ class Emission(_Emission):
             "gas phase": instance.gas_phase,
         }
         _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        return serialize_dict

musica/mechanism_configuration/first_order_loss.py

@@ -1,12 +1,17 @@
-from typing import Optional, Any, Dict, List, Union, Tuple
-from musica import _FirstOrderLoss, _ReactionComponent
-from .phase import Phase
-from .species import Species
+from .utils import _add_other_properties
 from .reactions import ReactionComponentSerializer
-from .utils import _add_other_properties, _remove_empty_keys
+from .species import Species
+from .phase import Phase
+from typing import Optional, Any, Dict, List, Union, Tuple
+from .. import backend
+
+_backend = backend.get_backend()
+_FirstOrderLoss = _backend._mechanism_configuration._FirstOrderLoss
+_ReactionComponent = _backend._mechanism_configuration._ReactionComponent
+ReactionType = _backend._mechanism_configuration._ReactionType
 
 
-class FirstOrderLoss(_FirstOrderLoss):
+class FirstOrderLoss:
     """
     A class representing a first-order loss reaction rate constant.
 
@@ -22,7 +27,8 @@ class FirstOrderLoss(_FirstOrderLoss):
         self,
         name: Optional[str] = None,
         scaling_factor: Optional[float] = None,
-        reactants: Optional[List[Union[Species, Tuple[float, Species]]]] = None,
+        reactants: Optional[List[Union[Species,
+                                       Tuple[float, Species]]]] = None,
         gas_phase: Optional[Phase] = None,
         other_properties: Optional[Dict[str, Any]] = None,
     ):
@@ -36,26 +42,127 @@ class FirstOrderLoss(_FirstOrderLoss):
             gas_phase (Phase): The gas phase in which the reaction occurs.
             other_properties (Dict[str, Any]): A dictionary of other properties of the first-order loss reaction rate constant.
         """
-        super().__init__()
-        self.name = name if name is not None else self.name
-        self.scaling_factor = scaling_factor if scaling_factor is not None else self.scaling_factor
-        self.reactants = (
-            [
-                (
-                    _ReactionComponent(r.name)
-                    if isinstance(r, Species)
-                    else _ReactionComponent(r[1].name, r[0])
-                )
-                for r in reactants
-            ]
-            if reactants is not None
-            else self.reactants
-        )
-        self.gas_phase = gas_phase.name if gas_phase is not None else self.gas_phase
-        self.other_properties = other_properties if other_properties is not None else self.other_properties
+        # Create the internal C++ instance
+        self._instance = _FirstOrderLoss()
+
+        # Set properties if provided
+        if name is not None:
+            self.name = name
+        if scaling_factor is not None:
+            self.scaling_factor = scaling_factor
+        if reactants is not None:
+            self.reactants = reactants
+        if gas_phase is not None:
+            self.gas_phase = gas_phase
+        if other_properties is not None:
+            self.other_properties = other_properties
+
+    @property
+    def name(self) -> str:
+        """Get the name."""
+        return self._instance.name
+
+    @name.setter
+    def name(self, value: str):
+        """Set the name."""
+        self._instance.name = value
+
+    @property
+    def scaling_factor(self) -> float:
+        """Get the scaling factor."""
+        return self._instance.scaling_factor
+
+    @scaling_factor.setter
+    def scaling_factor(self, value: float):
+        """Set the scaling factor."""
+        self._instance.scaling_factor = value
+
+    @property
+    def reactants(self) -> List[Union[Species, Tuple[float, Species]]]:
+        """Get the reactants as Python objects."""
+        # Convert from C++ _ReactionComponent objects to Python Species objects
+        result = []
+        for rc in self._instance.reactants:
+            if hasattr(rc, 'coefficient') and rc.coefficient != 1.0:
+                # Create a tuple with coefficient and species
+                species = Species(name=rc.species_name)
+                result.append((rc.coefficient, species))
+            else:
+                # Just the species
+                species = Species(name=rc.species_name)
+                result.append(species)
+        return result
+
+    @reactants.setter
+    def reactants(self, value: List[Union[Species, Tuple[float, Species]]]):
+        """Set the reactants, converting from Python to C++ objects."""
+        cpp_reactants = []
+        for r in value:
+            if isinstance(r, Species):
+                cpp_reactants.append(_ReactionComponent(r.name))
+            elif isinstance(r, tuple) and len(r) == 2:
+                coefficient, species = r
+                cpp_reactants.append(_ReactionComponent(species.name, coefficient))
+            else:
+                raise ValueError(f"Invalid reactant format: {r}")
+        self._instance.reactants = cpp_reactants
+
+    @property
+    def gas_phase(self) -> str:
+        """Get the gas phase name."""
+        return self._instance.gas_phase
+
+    @gas_phase.setter
+    def gas_phase(self, value: Union[Phase, str]):
+        """Set the gas phase."""
+        if isinstance(value, Phase):
+            self._instance.gas_phase = value.name
+        else:
+            self._instance.gas_phase = value
+
+    @property
+    def other_properties(self) -> Dict[str, Any]:
+        """Get the other properties."""
+        return self._instance.other_properties
+
+    @other_properties.setter
+    def other_properties(self, value: Dict[str, Any]):
+        """Set the other properties."""
+        self._instance.other_properties = value
+
+    @property
+    def type(self):
+        """Get the reaction type."""
+        return ReactionType.FirstOrderLoss
+
+    def serialize(self) -> Dict:
+        """
+        Serialize the FirstOrderLoss object to a dictionary using only Python-visible data.
+
+        Returns:
+            Dict: A dictionary representation of the FirstOrderLoss object.
+        """
+        serialize_dict = {
+            "type": "FIRST_ORDER_LOSS",
+            "name": self.name,
+            "scaling factor": self.scaling_factor,
+            "reactants": ReactionComponentSerializer.serialize_list_reaction_components(self._instance.reactants),
+            "gas phase": self.gas_phase,
+        }
+        _add_other_properties(serialize_dict, self.other_properties)
+        return _remove_empty_keys(serialize_dict)
 
     @staticmethod
-    def serialize(instance) -> Dict:
+    def serialize_static(instance) -> Dict:
+        """
+        Static serialize method for compatibility with C++ _FirstOrderLoss objects.
+
+        Args:
+            instance: The _FirstOrderLoss instance to serialize.
+
+        Returns:
+            Dict: A dictionary representation of the FirstOrderLoss object.
+        """
         serialize_dict = {
             "type": "FIRST_ORDER_LOSS",
             "name": instance.name,
@@ -64,4 +171,4 @@ class FirstOrderLoss(_FirstOrderLoss):
             "gas phase": instance.gas_phase,
         }
         _add_other_properties(serialize_dict, instance.other_properties)
-        return _remove_empty_keys(serialize_dict)
+        return serialize_dict